Multiple species of commensal microorganisms are harbored in the gastrointestinal (GI) tract of mammals, where they influence the development of the mucosal immune system leading to enhancement of protective functions of the mucous membranes and enabling the host to mount robust immune responses against pathogenic microbes invading the body, while staying non-responsive to dietary antigens and harmless microbes (Hooper et al., 2012, Science, 336:1268-73). Abnormality in the regulation of cross-talk between commensal bacteria and the immune system (GI dysbiosis) may lead to inflammatory and gastrointestinal conditions such as inflammatory bowel disease (IBD) ulcerative colitis, or Crohn's disease (U.S. Patent Appl. Pub. No. 20140341921 and references cited therein).
In addition to diverse populations of commensal bacterial species, the mammalian intestinal tract also hosts a broad variety of viruses that comprise the host's microvirome (Reyes et al., Nature 466, 334-338, (2010); Virgin, Cell 157, 142-150 (2014)).3,4. The coding potential of the enteric virome is predicted to be immense, because it includes viruses that infect host cells, endogenous retroviruses, and viruses that infect the various microbial inhabitants of the gastrointestinal tract, such as bacteria, archaea, and fungi. Recent studies indicate that the most abundant members of the enteric virome, bacteriophages that infect commensal bacteria, are diverse and likely to have a substantial impact on the host (Duerkop B A, Hooper L V. 2013. Nat. Immunol. 14:654-659).